Invoiced invoices can be marked as paid in the Payments -section. Go to Payments -section by clicking Billing -> Payments from the top menu.
The Payments -page shows a list of invoiced invoices. The Mark as Fully Paid -button is for each invoice. Click on it to mark the invoice as fully paid. The Add Payments -button can be used to add partial payment to the invoice, for example, in situation when only part of the invoice is paid.
Clicking Mark as Fully Paid -button will open the Add Payments -window where you can change the Execution, Sum and Type.
Select the date, enter the sum and select the type after which the transaction will be saved by clicking the Save Execution -button. The invoice automatically changes to the Paid state when the invoice is fully paid.